Debian Bug report logs - #1004053
kallisto: reproducible-builds: timestamps and build path embedded in test suite metadata

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Message #5 received at submit@bugs.debian.org (full text, mbox, reply):

From: Vagrant Cascadian <vagrant@reproducible-builds.org>

To: submit@bugs.debian.org

Subject: kallisto: reproducible-builds: timestamps and build path embedded in test suite metadata

Date: Wed, 19 Jan 2022 15:06:18 -0800

[Message part 1 (text/plain, inline)]

Source: kallisto
Severity: normal
Tags: patch
User: reproducible-builds@lists.alioth.debian.org
Usertags: buildpath timestamps
X-Debbugs-Cc: reproducible-bugs@lists.alioth.debian.org

Various files produced related to test suites embed timestamp and build
paths into the files, breaking reproducible builds:
  
  https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/diffoscope-results/kallisto.html

It looks like version 0.48.0+dfsg-1 introduced these new files, with the
introduction of the snakemake tests.

The attached patch fixes this by removing the test suite log files and
other test suite metadata in a dh_install override from debian/rules.

With this patch applied, kallisto should build reproducibly on
tests.reproducible-builds.org!

Thanks for maintaining kallisto!

live well,
  vagrant

[0001-debian-rules-Remove-various-test-suite-log-files-and.patch (text/x-diff, inline)]

From 5c5e9ba026cb5acb27cca8ede0ddc41015b879c4 Mon Sep 17 00:00:00 2001
From: Vagrant Cascadian <vagrant@reproducible-builds.org>
Date: Wed, 19 Jan 2022 22:58:14 +0000
Subject: [PATCH] debian/rules: Remove various test suite log files and
 metadata.

Various differences including timestamps, timing information, and
build paths are embedded in these files, which make it nearly
impossible to build the package reproducibly.

https://tests.reproducible-builds.org/debian/issues/unstable/test_suite_logs_issue.html
---
 debian/rules | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/debian/rules b/debian/rules
index 23ee80e..3d9a422 100755
--- a/debian/rules
+++ b/debian/rules
@@ -17,3 +17,10 @@ override_dh_auto_configure:
 override_dh_auto_test:
 	dh_auto_test
 	cd test && PATH=$$(find ../obj-* -name src):$(PATH) HOME=$$(mktemp --directory) snakemake --cores 1
+
+override_dh_install:
+	dh_install
+	# Remove test suite logs and other metadata about the test suite
+	rm -rvf debian/kallisto-examples/usr/share/doc/kallisto/test/.snakemake
+	rm -vf debian/kallisto-examples/usr/share/doc/kallisto/test/bus_out/run_info.json
+	rm -vf debian/kallisto-examples/usr/share/doc/kallisto/test/quant_out/run_info.json
-- 
2.34.1

[signature.asc (application/pgp-signature, inline)]

Message #8 received at 1004053-submitter@bugs.debian.org (full text, mbox, reply):

From: Andrius Merkys <noreply@salsa.debian.org>

To: 1004053-submitter@bugs.debian.org

Subject: Bug#1004053 marked as pending in kallisto

Date: Thu, 20 Jan 2022 06:47:33 +0000

Control: tag -1 pending

Hello,

Bug #1004053 in kallisto reported by you has been fixed in the
Git repository and is awaiting an upload. You can see the commit
message below and you can check the diff of the fix at:

https://salsa.debian.org/med-team/kallisto/-/commit/1b0c5ab8725a90417a23d1946d9ed60693231041

------------------------------------------------------------------------
Preventing volatile test outputs from appearing in kallisto-examples binary package (Closes: #1004053). Thanks Vagrant Cascadian.
------------------------------------------------------------------------

(this message was generated automatically)
-- 
Greetings

https://bugs.debian.org/1004053

Message #15 received at 1004053-close@bugs.debian.org (full text, mbox, reply):

From: Debian FTP Masters <ftpmaster@ftp-master.debian.org>

To: 1004053-close@bugs.debian.org

Subject: Bug#1004053: fixed in kallisto 0.48.0+dfsg-2

Date: Thu, 20 Jan 2022 07:34:05 +0000

Source: kallisto
Source-Version: 0.48.0+dfsg-2
Done: Andrius Merkys <merkys@debian.org>

We believe that the bug you reported is fixed in the latest version of
kallisto, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1004053@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andrius Merkys <merkys@debian.org> (supplier of updated kallisto package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Thu, 20 Jan 2022 02:09:50 -0500
Source: kallisto
Architecture: source
Version: 0.48.0+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andrius Merkys <merkys@debian.org>
Closes: 1004053
Changes:
 kallisto (0.48.0+dfsg-2) unstable; urgency=medium
 .
   * Team upload.
   * Preventing volatile test outputs from appearing in kallisto-examples
     binary package (Closes: #1004053). Thanks Vagrant Cascadian.
   * Limiting kallisto builds to 64bit architectures as 32bit are not supported.
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 2781925a650facd11e3833ba4ec9b324e5e5a505 7173 kallisto_0.48.0+dfsg-2_source.buildinfo
Checksums-Sha256:
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 afa297ebe5078baee8888f9bc398eb2372f991a884f1968c7c6d6caa20941f8c 7016 kallisto_0.48.0+dfsg-2.debian.tar.xz
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Files:
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 3542de36a8f22b9ebe0f452f420d1ae1 7016 science optional kallisto_0.48.0+dfsg-2.debian.tar.xz
 f30ec101c5bd1a6f213bf9a922de66c1 7173 science optional kallisto_0.48.0+dfsg-2_source.buildinfo

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Message #20 received at 1004053@bugs.debian.org (full text, mbox, reply):

From: Vagrant Cascadian <vagrant@reproducible-builds.org>

To: 1004053@bugs.debian.org

Subject: Re: Bug#1004053: marked as pending in kallisto

Date: Thu, 20 Jan 2022 16:28:04 -0800

On 2022-01-20, Andrius Merkys wrote:
> Bug #1004053 in kallisto reported by you has been fixed in the
> Git repository and is awaiting an upload. You can see the commit
> message below and you can check the diff of the fix at:
>
> https://salsa.debian.org/med-team/kallisto/-/commit/1b0c5ab8725a90417a23d1946d9ed60693231041
>
> ------------------------------------------------------------------------
> Preventing volatile test outputs from appearing in kallisto-examples binary package (Closes: #1004053). Thanks Vagrant Cascadian.
> ------------------------------------------------------------------------

Thanks!

The fix applied didn't catch all of the issues, there are still
timestamps in run_info.json:

  https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/diffoscope-results/kallisto.html

  ./usr/share/doc/kallisto/test/quant_out/run_info.json

  "start_time":·"Wed·Jan·19·22:31:09·2022"
  vs.
  "start_time":·"Thu·Feb·23·06:45:29·2023"


I presume you could either remove that file, or sanitize out the
timestamp.


Just a one-line difference, left! :)


live well,
  vagrant

Message #33 received at 1004053@bugs.debian.org (full text, mbox, reply):

From: Vagrant Cascadian <vagrant@reproducible-builds.org>

To: 1004053@bugs.debian.org

Subject: Re: Bug#1004053: kallisto: reproducible-builds: timestamps and build path embedded in test suite metadata

Date: Tue, 11 Apr 2023 15:25:42 -0700

[Message part 1 (text/plain, inline)]

>> On 2022-01-20, Vagrant Cascadian wrote:
>>> The fix applied didn't catch all of the issues, there are still
>>> timestamps in run_info.json:
>>>
>>>   https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/diffoscope-results/kallisto.html
>>>
>>>   ./usr/share/doc/kallisto/test/quant_out/run_info.json
>>>
>>>   "start_time":·"Wed·Jan·19·22:31:09·2022"
>>>   vs.
>>>   "start_time":·"Thu·Feb·23·06:45:29·2023"
>>>
>>>
>>> I presume you could either remove that file, or sanitize out the
>>> timestamp.

Attached is a patch against the current package that should fix the
remaining issue.

Thanks for maintaining kallisto!

live well,
  vagrant

[0001-debian-rules-Remove-quant_out-run_info.json-Closes-1.patch (text/x-diff, inline)]

From c42589d13a1bef7f16d2164e4bc9baac00e7ab94 Mon Sep 17 00:00:00 2001
From: Vagrant Cascadian <vagrant@reproducible-builds.org>
Date: Tue, 11 Apr 2023 15:21:14 -0700
Subject: [PATCH] debian/rules: Remove quant_out/run_info.json (Closes:
 #1004053).

---
 debian/rules | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/debian/rules b/debian/rules
index f4fadaa..221d06c 100755
--- a/debian/rules
+++ b/debian/rules
@@ -17,4 +17,4 @@ override_dh_auto_configure:
 override_dh_auto_test:
 	dh_auto_test
 	cd test && PATH=$$(find ../obj-* -name src):$(PATH) HOME=$$(mktemp --directory) snakemake --cores 1
-	rm -rf test/.snakemake test/bus_out test/transcripts.kidx.gz
+	rm -rf test/.snakemake test/bus_out test/quant_out/run_info.json test/transcripts.kidx.gz
-- 
2.39.2

[signature.asc (application/pgp-signature, inline)]

Message #38 received at 1004053-close@bugs.debian.org (full text, mbox, reply):

From: Debian FTP Masters <ftpmaster@ftp-master.debian.org>

To: 1004053-close@bugs.debian.org

Subject: Bug#1004053: fixed in kallisto 0.48.0+dfsg-4

Date: Wed, 12 Apr 2023 06:49:21 +0000

Source: kallisto
Source-Version: 0.48.0+dfsg-4
Done: Andreas Tille <tille@debian.org>

We believe that the bug you reported is fixed in the latest version of
kallisto, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1004053@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated kallisto package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Wed, 12 Apr 2023 07:44:19 +0200
Source: kallisto
Architecture: source
Version: 0.48.0+dfsg-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Closes: 1004053
Changes:
 kallisto (0.48.0+dfsg-4) unstable; urgency=medium
 .
   [ Vagrant Cascadian ]
   * Remove quant_out/run_info.json to enable reproducible-builds
     Closes: #1004053
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